Project description:Seasonal influenza outbreaks represent a large burden for the healthcare system as well as the economy. While the role of the microbiome in the context of various diseases has been elucidated, the effects on the respiratory and gastrointestinal microbiome during influenza illness is largely unknown. Therefore, this study aimed to characterize the temporal development of the respiratory and gastrointestinal microbiome of swine using a multi-omics approach prior and during influenza infection. Swine is a suitable animal model for influenza research, as it is closely related to humans and a natural host for influenza viruses. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae families in the upper respiratory tract. To our surprise, temporal development of the respiratory microbiome was not affected. Furthermore, we observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, we found increased abundances of Prevotellaceae, while Clostridiaceae and Lachnospiraceae decreased. Furthermore, metaproteomics showed that the functional composition of the microbiome, known to be robust and stable under healthy conditions, was heavily affected by the influenza infection. Metabolome analysis proved increased amounts of short-chain fatty acids in the gastrointestinal tract, which might be involved in faster recovery. Furthermore, metaproteome data suggest a possible immune response towards flagellated Clostridia induced during the infection. Therefore, it can be assumed that the respiratory infection with IAV caused a systemic effect in the porcine host and microbiome.
Project description:Human subjects were vaccinated with seasonal influenza vaccine (TIV, 2014-2015). We then used scATAC-seq to construct the single-cell landscape of the innate immune response to TIV at the epigenomic level. PBMCs from vaccinated individuals were isolated at day 0, 1, and 30, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell chromatin accessibility profiling.
Project description:Human subjects were vaccinated with seasonal influenza vaccine at day 0 (TIV, 2014-2015). A subgroup of subjects (abx) received an additional oral antibiotic regimen, consisting of neomycin, vancomycin, and metronidazole, between days -3 and 1. CD14+ monocytes, mDCs, and pDCs were isolated from PBMCs of vaccinated subjects (3 antibiotic treated, 5 controls) at day -21 (BL), 0 and 30 using FACS. ATAC-seq was used to analyze the chromatin accessibility landscape in these cells.
Project description:Human subjects were vaccinated with seasonal influenza vaccine (TIV, 2014-2015). We then used scRNA-seq to constructed the single-cell landscape of the innate immune response to TIV at the transcriptional level. PBMCs from vaccinated individuals were isolated at day 0, 1, and 30, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell gene expression profiling.
Project description:Human subjects were vaccinated with seasonal influenza vaccine at day 0 (TIV, 2014-2015). A subgroup of subjects (abx) received an additional oral antibiotic regimen, consisting of neomycin, vancomycin, and metronidazole, between days -3 and 1. CD14+ monocytes were isolated from PBMCs of vaccinated subjects (2 antibiotic treated, 3 controls) at day 0 and 30 using FACS. RNA-seq was used to analyze the transcriptional landscape in these cells.
Project description:Viral infections affecting the upper or lower respiratory tract induce mucin production in the epithelial surfaces of the respiratory cells. However, a little is known about how mucins are produced on the surfaces of respiratory epithelial cells and affects viral replication. In the course of the investigation of the cellular responses in the early stage of Influenza A virus (IAV) infection, we found that two miRNAs, miR-221 and miR-17-3p, which target the mRNA of GalNAc transferase 3 (GALNT3), are rapidly down-regulated as early as 1.5 h post-infection. To understand the early host cell responses to the IAV infection, we performed miRNA microarray analysis using a human alveolar adenocarcinoma cell line, A549 cells, infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus. We isolated the cellular RNAs at 0.5, 1.5 and 4.5 h post-infection and detected significant changes in the global profile of miRNA expression after infection with IAV. mouse embryonic fibroblasts. Each sample was run in duplicate.
Project description:Human tracheobronchial epithelial (HTBE) cells are considered to serve as a good correlate of influenza virus infection in the human respiratory tract. ChIP-Seq analysis was used to profile histone acetylation (H3K27ac) in HTBE cells at multiple time points in response to infection with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus. The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53.
